For a project I’m on, I was investigating software for simulation of biological processes and systems. I was interested in the virtual cell simulation software earlier this year. And I think the virtual worm is really quite amazing. And when I investigated GenoCAD I saw that their simulation feature was based on the COPASI software: a COmplex PAthway SImulator. So I went looking for more information about their tools.
The original publication (below) was a nice introduction to the concepts and the foundation. They continue to develop COPASI and others are using it as well. One of the things I really like to see is an active mailing list or forum where people are talking about what they are doing, and COPASI has that too.
A nice way to get started with what COPASI can do is to have a look at their videos. They have a page with several of them. I’ll just put the introduction one here, but the others are also very nice to see more of the specifics of working with their interface. Go over to their Video Tutorials page to see the others.
COPASI videos: http://www.copasi.org/VideoTutorials
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U. (2006). COPASI–a COmplex PAthway SImulator Bioinformatics, 22 (24), 3067-3074 DOI: 10.1093/bioinformatics/btl485